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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 04, 2010 |
| Title |
ESHyb_H31S31_HA_H3K36me3_xChIPSeq |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain/genotype: 129SvJae x M. m. castaneus F1 H3.1S31-HA / H3.3B
cell type: F1 hybrid "965" embryonic stem cells
chip antibody: H3K36me3 (Abcam ab9050)
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| Growth protocol |
For early passages, ES cells were maintained on mitomycin C treated feeders in standard ES cell media, KO-DMEM (Invitrogen 10829-018), 2mM L-glutamine (Sigma G7513) and pen-strep, 15% ES grade fetal bovine serum (Gibco 10439-024), 10-4 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF). To remove feeders for ChIP or NPC differentiation, ES cells were passaged at least two passages off of feeders on to gelatin-coated plates. ES cells were differentiated to NPCs by re-plating d7 adherent neural differentiation cultures (typically 2–3 × 10^6 cells) into an uncoated T75 flask in NS-A medium as described (Conti et al., 2005). To expand NPCs for ChIP, NPCs were cultured on gelatin-coated plates in NeuroCult NSC Basal Medium (Mouse, Stem Cell Technologies) supplemented with 2mM final L-glutamine and pen-strep (Omega Scientific), modified N2 supplement freshly prepared in house as described (Conti et al., 2005), and 10ng/ml of both mouse EGF and human FGF-2 (Peprotech).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinking ChIP was performed as described (Lee et al. 2006), with minor modifications as described in Goldberg, et al. 2010. Briefly, ES cells and NPCs were harvested and fixed in 1% paraformaldehyde, pellets flash-frozen in liquid nitrogen, and stored at -80 degrees C. Chromatin was isolated and sheared to 200-700 bp using a Bioruptor (Diagenode), and ChIP was performed as described (Lee et al. 2006). Native ChIP was performed as described (Barski et al. 2007), with minor modifications as described in Goldberg, et al. 2010. Following isolation of ChIP DNA, libraries were prepared for cluster generation as described (Goldberg et al. 2010). Purified DNA libraries were used for cluster generation on Illumina/Solexa flow cells, and sequencing analysis was performed on an Illumina/Solexa Genome Analyzer 2 following manufacturer protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
sample 18
Crosslinking chromatin IP (xChIP) against H3K36me3
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| Data processing |
BED files were generated from alignment files by keeping unique reads mapped to a single best-matching location with no more than two mismatches. The UCSC mm9 was used for the alignments.
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| Submission date |
Dec 18, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron D Goldberg |
| Organization name |
The Rockefeller University
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| Department |
Laboratory of Chromatin Biology
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| Lab |
Allis Laboratory
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| Street address |
1230 York Avenue - Box 78
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE16893 |
Distinct factors control histone variant H3.3 localization at specific genomic regions |
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| Relations |
| SRA |
SRX016844 |
| BioSample |
SAMN00008986 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM487543_s1_965_H3dot1_S31_HA_K36me3_bed.txt.gz |
45.3 Mb |
(ftp)(http) |
TXT |
| GSM487543_s1_965_H3dot1_S31_HA_K36me3_eland_extended.txt.gz |
240.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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